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liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data
MIT License
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fastq-extractor": No such file or directory #317

Open origami974 opened 1 month ago

origami974 commented 1 month ago

Dear Doctor Today, my TRUST4 suddenly had a small problem:/ run-trust4 -f hg38_bcrtcr.fa --ref human_IMGT+C.fa -1 /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_2.fastq.gz -2 /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_3.fastq --barcode /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_2.fastq.gz --readFormat bc:0:15

Then I encountered this type of error: [Fri Oct 11 11:35:00 2024] SYSTEM CALL: /data/zhanqh/TRUST4/TRUST4/fastq-extractor -t 1 -f hg38_bcrtcr.fa -o TRUST_SRR29767032_3_toassemble --readFormat bc:0:15 -1 /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_3.fastq.gz -2 /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_3.fastq --barcode /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_2.fastq.gz Can't exec "/data/zhanqh/TRUST4/TRUST4/fastq-extractor": No such file or directory at ./run-trust4 line 59. system /data/zhanqh/TRUST4/TRUST4/fastq-extractor -t 1 -f hg38_bcrtcr.fa -o TRUST_SRR29767032_3_toassemble --readFormat bc:0:15 -1 /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_3.fastq.gz -2 /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_3.fastq --barcode /data/zhanqh/data_all/SRR_data/SRR29767032/SRR29767032_2.fastq.gz failed: -1 at ./run-trust4 line 59.

I first tried reinstalling, but it didn't seem to solve the problem， and then tried modifying FastqExtractor.cpp to fastq-extractor, but the result prompted me: Can't exec "/data/zhanqh/TRUST4/TRUST4/fastq-extractor": Permission denied at /data/zhanqh/TRUST4/TRUST4/run-trust4 line 59. I am a bit confused now and I hope to receive your guidance

origami974 commented 1 month ago

When I tried to run the sample file, I still encountered this error： ./run-trust4 -f human_IMGT+C.fa --ref human_IMGT+C.fa -1 example/example_1.fq -2 example/example_2.fq -o TRUST_example [Fri Oct 11 12:02:39 2024] TRUST4 v1.1.5-r549 begins. [Fri Oct 11 12:02:39 2024] SYSTEM CALL: /data/zhanqh/TRUST4/TRUST4/fastq-extractor -t 1 -f human_IMGT+C.fa -o TRUST_example_toassemble -1 example/example_1.fq -2 example/example_2.fq Can't exec "/data/zhanqh/TRUST4/TRUST4/fastq-extractor": No such file or directory at ./run-trust4 line 59. system /data/zhanqh/TRUST4/TRUST4/fastq-extractor -t 1 -f human_IMGT+C.fa -o TRUST_example_toassemble -1 example/example_1.fq -2 example/example_2.fq failed: -1 at ./run-trust4 line 59.

mourisl commented 1 month ago

You need to run "make" to compile TRUST4 from the source code to obtain the executable files like "fastq-extractor" first. The alternative approach is to install TRUST4 through conda as README instructs.